CombineMols is a python package for easily combining two molecules.
This intuitively aids in the combining of molecules using dummy atoms.
The easiest way to install the dependencies is to install the Anaconda 3 Python distribution and use conda to set up an environment with RDKit.
rdkit / mendeleev
Make a new conda environment and install RDKit.
conda create -c rdkit -n my-rdkit-env rdkit
Then activate this new environment.
conda activate my-rdkit-env
Inside this environment install CombineMols.
Using pip
pip install CombineMols
from rdkit import Chem
from CombineMols.CombineMols import CombineMols
Two molecule classes can be combined.
mol1 = Chem.MolFromSmiles('IOc1c[nH]c2ncc(I)cc12')
mol2 = Chem.MolFromSmiles('Sc1cccc(I)c1I')
CombineMols(mol1, mol2, "I")
Molecules can be entered directly in SMILES form.
mol1 = 'IOc1c[nH]c2ncc(I)cc12'
mol2 = 'Sc1cccc(I)c1I'
CombineMols(mol1, mol2, "I")
Dummy atom can be entered by atomic number.
mol1 = 'IOc1c[nH]c2ncc(I)cc12'
mol2 = 'Sc1cccc(I)c1I'
CombineMols(mol1, mol2, 53)